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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
Package 11/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
affylmGUI1.11.4Keith SatterleyLast Changed Date: 2007-06-25 07:29:21 -0700 Last Changed Rev: 25542 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
wellington | Linux (SUSE 9.2) | i686 | OK | OK | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | OK | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | [ OK ] | OK |
Package: affylmGUI |
Version: 1.11.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check affylmGUI_1.11.4.tar.gz |
RetCode: 0 |
Time: 77.2 seconds |
Status: OK |
CheckDir: affylmGUI.Rcheck |
Warnings: 0 |
* checking for working latex ... OK * using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/affylmGUI.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-08-10 r42465) * checking for file 'affylmGUI/DESCRIPTION' ... OK * this is package 'affylmGUI' version '1.11.4' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'affylmGUI' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ChooseCDF: no visible binding for global variable '.affylmGUIglobals' ChooseCDF : onOK: no visible binding for global variable '.affylmGUIglobals' ChooseCDF : onOK: no visible binding for global variable 'cdfDataFrame' ChooseCDF : onCancel: no visible binding for global variable '.affylmGUIglobals' ChooseCDF : <anonymous>: no visible binding for global variable '.affylmGUIglobals' ChooseContrastParameterization: no visible binding for global variable 'affylmGUIenvironment' ChooseContrastParameterization: no visible binding for global variable '.affylmGUIglobals' ChooseContrastParameterization : onOK: no visible binding for global variable '.affylmGUIglobals' ChooseContrastParameterization : onCancel: no visible binding for global variable '.affylmGUIglobals' ChooseContrastParameterization : <anonymous>: no visible binding for global variable '.affylmGUIglobals' ChooseEbayesStatistic: no visible binding for global variable '.affylmGUIglobals' ChooseEbayesStatistic : onOK: no visible binding for global variable '.affylmGUIglobals' ChooseEbayesStatistic : onCancel: no visible binding for global variable '.affylmGUIglobals' ChooseEbayesStatistic : <anonymous>: no visible binding for global variable '.affylmGUIglobals' ComputeContrasts: no visible binding for global variable 'affylmGUIenvironment' ComputeLinearModelFit: no visible binding for global variable 'affylmGUIenvironment' ComputeLinearModelFit: no visible binding for global variable '.affylmGUIglobals' DeleteContrastParameterization: no visible binding for global variable 'affylmGUIenvironment' DensityPlot: no visible binding for global variable 'affylmGUIenvironment' DensityPlot: no visible binding for global variable '.affylmGUIglobals' DensityPlot : plotFunction: no visible binding for global variable '.affylmGUIglobals' DensityPlotAll: no visible binding for global variable 'affylmGUIenvironment' DensityPlotAll: no visible binding for global variable '.affylmGUIglobals' DensityPlotAll : plotFunction: no visible binding for global variable '.affylmGUIglobals' DensityPlotAll : plotFunction: no visible binding for global variable 'affylmGUIenvironment' ExportHTMLreport: no visible binding for global variable 'affylmGUIenvironment' ExportNormalizedExpressionValues: no visible binding for global variable 'affylmGUIenvironment' GetComponentsToExportInHTMLreport: no visible binding for global variable 'affylmGUIenvironment' GetComponentsToExportInHTMLreport: no visible binding for global variable '.affylmGUIglobals' GetComponentsToExportInHTMLreport : onOK: no visible binding for global variable '.affylmGUIglobals' GetComponentsToExportInHTMLreport : onCancel: no visible binding for global variable '.affylmGUIglobals' GetComponentsToExportInHTMLreport : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetContrast: no visible binding for global variable '.affylmGUIglobals' GetContrast: no visible binding for global variable 'affylmGUIenvironment' GetContrast : onOK: no visible binding for global variable '.affylmGUIglobals' GetContrast : onCancel: no visible binding for global variable '.affylmGUIglobals' GetContrast : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetContrastNamesForHeatDiagram: no visible binding for global variable '.affylmGUIglobals' GetContrastNamesForHeatDiagram : onOK: no visible binding for global variable '.affylmGUIglobals' GetContrastNamesForHeatDiagram : onCancel: no visible binding for global variable '.affylmGUIglobals' GetContrastNamesForHeatDiagram : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetContrastParameterizationName: no visible binding for global variable '.affylmGUIglobals' GetContrastParameterizationName : onOK: no visible binding for global variable '.affylmGUIglobals' GetContrastParameterizationName : onCancel: no visible binding for global variable '.affylmGUIglobals' GetContrastParameterizationName : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetContrasts: no visible binding for global variable 'affylmGUIenvironment' GetDEcutoff: no visible binding for global variable '.affylmGUIglobals' GetDEcutoff : onOK: no visible binding for global variable '.affylmGUIglobals' GetDEcutoff : onCancel: no visible binding for global variable '.affylmGUIglobals' GetDEcutoff : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetGeneLabelsOptions: no visible binding for global variable '.affylmGUIglobals' GetGeneLabelsOptions : onOK: no visible binding for global variable '.affylmGUIglobals' GetGeneLabelsOptions : onCancel: no visible binding for global variable '.affylmGUIglobals' GetGeneLabelsOptions : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetJpegOrPngParams: no visible binding for global variable '.affylmGUIglobals' GetJpegOrPngParams : onOK: no visible binding for global variable '.affylmGUIglobals' GetJpegOrPngParams : onCancel: no visible binding for global variable '.affylmGUIglobals' GetJpegOrPngParams : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetJpegOrPngX11Params: no visible binding for global variable '.affylmGUIglobals' GetJpegOrPngX11Params : onOK: no visible binding for global variable '.affylmGUIglobals' GetJpegOrPngX11Params : onCancel: no visible binding for global variable '.affylmGUIglobals' GetJpegOrPngX11Params : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetLogPLMDataChoice: no visible binding for global variable '.affylmGUIglobals' GetLogPLMDataChoice : onCancel: no visible binding for global variable '.affylmGUIglobals' GetLogPLMDataChoice : onOK: no visible binding for global variable '.affylmGUIglobals' GetLogPLMDataChoice : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetMultipleContrasts: no visible binding for global variable '.affylmGUIglobals' GetMultipleContrasts: no visible binding for global variable 'affylmGUIenvironment' GetMultipleContrasts : onOK: no visible binding for global variable '.affylmGUIglobals' GetMultipleContrasts : onCancel: no visible binding for global variable '.affylmGUIglobals' GetMultipleContrasts : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetNormalizationMethod: no visible binding for global variable '.affylmGUIglobals' GetNormalizationMethod : onCancel: no visible binding for global variable '.affylmGUIglobals' GetNormalizationMethod : onOK: no visible binding for global variable '.affylmGUIglobals' GetNormalizationMethod : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetPValueCutoff: no visible binding for global variable '.affylmGUIglobals' GetPValueCutoff : onOK: no visible binding for global variable '.affylmGUIglobals' GetPValueCutoff : onCancel: no visible binding for global variable '.affylmGUIglobals' GetPValueCutoff : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetParameterizationName: no visible binding for global variable '.affylmGUIglobals' GetParameterizationName : onOK: no visible binding for global variable '.affylmGUIglobals' GetParameterizationName : onCancel: no visible binding for global variable '.affylmGUIglobals' GetParameterizationName : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetPlotLabels: no visible binding for global variable '.affylmGUIglobals' GetPlotLabels : onOK: no visible binding for global variable '.affylmGUIglobals' GetPlotLabels : onCancel: no visible binding for global variable '.affylmGUIglobals' GetPlotLabels : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetPlotSize: no visible binding for global variable '.affylmGUIglobals' GetPlotSize : onOK: no visible binding for global variable '.affylmGUIglobals' GetPlotSize : onCancel: no visible binding for global variable '.affylmGUIglobals' GetPlotSize : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetPlotTitle: no visible binding for global variable '.affylmGUIglobals' GetPlotTitle : onOK: no visible binding for global variable '.affylmGUIglobals' GetPlotTitle : onCancel: no visible binding for global variable '.affylmGUIglobals' GetPlotTitle : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetResidualTypeChoice: no visible binding for global variable '.affylmGUIglobals' GetResidualTypeChoice : onCancel: no visible binding for global variable '.affylmGUIglobals' GetResidualTypeChoice : onOK: no visible binding for global variable '.affylmGUIglobals' GetResidualTypeChoice : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetSetNames: no visible binding for global variable '.affylmGUIglobals' GetSetNames : onOK: no visible binding for global variable '.affylmGUIglobals' GetSetNames : onCancel: no visible binding for global variable '.affylmGUIglobals' GetSetNames : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetSlideNum: no visible binding for global variable 'affylmGUIenvironment' GetSlideNum: no visible binding for global variable '.affylmGUIglobals' GetSlideNum : onOK: no visible binding for global variable '.affylmGUIglobals' GetSlideNum : onCancel: no visible binding for global variable '.affylmGUIglobals' GetSlideNum : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetSlideNums: no visible binding for global variable 'affylmGUIenvironment' GetSlideNums: no visible binding for global variable '.affylmGUIglobals' GetSlideNums : onOK: no visible binding for global variable '.affylmGUIglobals' GetSlideNums : onCancel: no visible binding for global variable '.affylmGUIglobals' GetSlideNums : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetWhichProbes: no visible binding for global variable '.affylmGUIglobals' GetWhichProbes : onCancel: no visible binding for global variable '.affylmGUIglobals' GetWhichProbes : onOK: no visible binding for global variable '.affylmGUIglobals' GetWhichProbes : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetWtAreaParams: no visible binding for global variable '.affylmGUIglobals' GetWtAreaParams : onOK: no visible binding for global variable 'affylmGUIenvironment' GetWtAreaParams : onOK: no visible binding for global variable '.affylmGUIglobals' GetWtAreaParams : onCancel: no visible binding for global variable '.affylmGUIglobals' GetWtAreaParams : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetWtFlagParams: no visible binding for global variable '.affylmGUIglobals' GetWtFlagParams : onOK: no visible binding for global variable '.affylmGUIglobals' GetWtFlagParams : onCancel: no visible binding for global variable '.affylmGUIglobals' GetWtFlagParams : <anonymous>: no visible binding for global variable '.affylmGUIglobals' GetWtFlagParams: no visible binding for global variable 'affylmGUIenvironment' GetlimmaDataSetName: no visible binding for global variable 'affylmGUIenvironment' GetlimmaDataSetName: no visible binding for global variable '.affylmGUIglobals' GetlimmaDataSetName : onOK: no visible binding for global variable 'affylmGUIenvironment' GetlimmaDataSetName : <anonymous>: no visible binding for global variable '.affylmGUIglobals' HTMLplotUsingFunction: no visible binding for global variable '.HTML.file' HTMLplotUsingFunction: no visible binding for global variable 'gif' HeatDiagramDialog: no visible binding for global variable '.affylmGUIglobals' HeatDiagramDialog : onOK: no visible binding for global variable '.affylmGUIglobals' HeatDiagramDialog : onCancel: no visible binding for global variable '.affylmGUIglobals' HeatDiagramDialog : <anonymous>: no visible binding for global variable '.affylmGUIglobals' HeatDiagramPlot: no visible binding for global variable 'affylmGUIenvironment' ImageArrayPlot: no visible binding for global variable 'affylmGUIenvironment' ImageArrayPlot: no visible binding for global variable '.affylmGUIglobals' ImageArrayPlot : plotFunction: no visible binding for global variable '.affylmGUIglobals' ImageQualityResidualPlot: no visible binding for global variable 'affylmGUIenvironment' ImageQualityResidualPlot: no visible binding for global variable '.affylmGUIglobals' ImageQualityResidualPlot : plotFunction: no visible binding for global variable '.affylmGUIglobals' ImageQualityWeightPlot: no visible binding for global variable 'affylmGUIenvironment' ImageQualityWeightPlot: no visible binding for global variable '.affylmGUIglobals' ImageQualityWeightPlot : plotFunction: no visible binding for global variable '.affylmGUIglobals' IntensityHistogram: no visible binding for global variable 'affylmGUIenvironment' IntensityHistogram: no visible binding for global variable '.affylmGUIglobals' IntensityHistogram : plotFunction: no visible binding for global variable '.affylmGUIglobals' IntensityHistogramAll: no visible binding for global variable 'affylmGUIenvironment' IntensityHistogramAll: no visible binding for global variable '.affylmGUIglobals' IntensityHistogramAll : plotFunction: no visible binding for global variable '.affylmGUIglobals' LogOddsPlot: no visible binding for global variable 'affylmGUIenvironment' NUSEPlotAll: no visible binding for global variable 'affylmGUIenvironment' NUSEPlotAll: no visible binding for global variable '.affylmGUIglobals' NUSEPlotAll : plotFunction: no visible binding for global variable '.affylmGUIglobals' NewLimmaFile: no visible binding for global variable 'affylmGUIenvironment' NormalizeNow: no visible binding for global variable 'affylmGUIenvironment' NormalizeNow: no visible binding for global variable '.affylmGUIglobals' NormalizedIntensityBoxPlot: no visible binding for global variable 'affylmGUIenvironment' NormalizedIntensityBoxPlot: no visible binding for global variable '.affylmGUIglobals' NormalizedIntensityBoxPlot : plotFunction: no visible binding for global variable '.affylmGUIglobals' OpenALimmaFile: no visible binding for global variable 'affylmGUIenvironment' OpenCDFFile: no visible binding for global variable 'cdf' OpenCDFFile: no visible binding for global variable 'affylmGUIenvironment' OpenCDFandTargetsfiles : onOK: no visible binding for global variable 'affylmGUIenvironment' OpenCDFandTargetsfiles: no visible binding for global variable 'affylmGUIenvironment' OpenTargetsFile: no visible binding for global variable 'affylmGUIenvironment' PlotOptions: no visible binding for global variable '.affylmGUIglobals' PlotOptions : onOK: no visible binding for global variable '.affylmGUIglobals' PlotOptions : <anonymous>: no visible binding for global variable '.affylmGUIglobals' QQTplot: no visible binding for global variable 'affylmGUIenvironment' RLEPlotAll: no visible binding for global variable 'affylmGUIenvironment' RLEPlotAll: no visible binding for global variable '.affylmGUIglobals' RLEPlotAll : plotFunction: no visible binding for global variable '.affylmGUIglobals' RNADegradationPlotAll: no visible binding for global variable 'affylmGUIenvironment' RNADegradationPlotAll: no visible binding for global variable '.affylmGUIglobals' RNADegradationPlotAll : plotFunction: no visible binding for global variable '.affylmGUIglobals' RawIntensityBoxPlot: no visible binding for global variable 'affylmGUIenvironment' RawIntensityBoxPlot: no visible binding for global variable '.affylmGUIglobals' RawIntensityBoxPlot : plotFunction: no visible binding for global variable '.affylmGUIglobals' Resize: no visible binding for '<<-' assignment to 'LocalHScale' Resize: no visible binding for '<<-' assignment to 'LocalVScale' Resize: no visible binding for global variable 'LocalHScale' Resize: no visible binding for global variable 'LocalVScale' SaveAsLimmaFile: no visible binding for global variable 'affylmGUIenvironment' SaveAsLimmaFile: no visible binding for global variable '.affylmGUIglobals' SaveLimmaFile: no visible binding for global variable 'affylmGUIenvironment' SaveLimmaFile: no visible binding for global variable '.affylmGUIglobals' SetWD: no visible binding for global variable '.affylmGUIglobals' TclRequire: no visible binding for global variable '.affylmGUIglobals' TclRequire : onDestroy: no visible binding for global variable '.affylmGUIglobals' TclRequire : onOK: no visible binding for global variable '.affylmGUIglobals' TclRequire : onOK: no visible binding for global variable 'affylmGUIenvironment' UpDownOrBoth: no visible binding for global variable '.affylmGUIglobals' UpDownOrBoth : onOK: no visible binding for global variable '.affylmGUIglobals' UpDownOrBoth : <anonymous>: no visible binding for global variable '.affylmGUIglobals' VennDiagramPlot: no visible binding for global variable 'affylmGUIenvironment' ViewContrastsMatrixAsPairs: no visible binding for global variable 'affylmGUIenvironment' ViewContrastsMatrixInTable: no visible binding for global variable 'affylmGUIenvironment' ViewExistingContrastParameterization: no visible binding for global variable 'affylmGUIenvironment' ViewExistingContrastParameterization: possible error in ViewContrastsMatrixInTable(contrastsMatrix = "Contrasts", contrastsList, contrastParameterizationIndex): unused argument(s) (contrastParameterizationIndex) ViewRNATargets: no visible binding for global variable 'affylmGUIenvironment' ViewRNATargets: no visible binding for global variable '.affylmGUIglobals' ViewRNATargets : onClose: no visible binding for global variable '.affylmGUIglobals' ViewRNATargets : <anonymous>: no visible binding for global variable '.affylmGUIglobals' affyPlotMA: no visible binding for global variable 'affylmGUIenvironment' affyPlotMA: no visible binding for global variable '.affylmGUIglobals' affyPlotMA : plotFunction: no visible binding for global variable '.affylmGUIglobals' affyPlotMAcontrast: no visible binding for global variable 'affylmGUIenvironment' affylmGUI: no visible binding for global variable 'affylmGUIenvironment' affylmGUI: no visible binding for global variable '.affylmGUIglobals' affylmGUI : <anonymous>: no visible binding for global variable '.affylmGUIglobals' chooseDir: no visible binding for global variable '.affylmGUIglobals' evalRcode: no visible binding for global variable '.affylmGUIglobals' evalRcode : runOverall: no visible binding for global variable '.affylmGUIglobals' evalRcode : runOverall: no visible binding for global variable 'affylmGUIenvironment' evalRcode : runOverall: no visible binding for global variable 'tmpEvalRcodeResultsGraph' generalPlotFunction: no visible binding for global variable '.affylmGUIglobals' generalPlotFunction: no visible binding for global variable 'affylmGUIenvironment' initGlobals: no visible binding for global variable 'affylmGUIenvironment' onDestroy: no visible binding for global variable 'affylmGUIenvironment' onExit: no visible binding for global variable 'affylmGUIenvironment' onExit: no visible binding for global variable '.affylmGUIglobals' showTopTable: no visible binding for global variable 'affylmGUIenvironment' * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * creating affylmGUI-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating affylmGUI-manual.tex ... OK * checking affylmGUI-manual.tex ... OK
affylmGUI.Rcheck/00install.out:
* Installing *source* package 'affylmGUI' ... ** R ** inst ** preparing package for lazy loading Loading required package: limma Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio Loading required package: preprocessCore ** help >>> Building/Updating help pages for package 'affylmGUI' Formats: text html latex example ALGchangeLog text html latex affylmGUI text html latex ** building package indices ... * DONE (affylmGUI)